Browsing by Author "Itan, Y."

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Open Access
The genetic structure of the Turkish population reveals high levels of variation and admixture
(National Academy of Sciences, 2020-12-18) Kars, Meltem Ece; Başak, A. N.; Onat, Onur Emre; Bilguvar, K.; Choi, J.; Itan, Y.; Çağlar, C.; Palvadeau, R.; Casanova, J.-L.; Cooper, D. N.; Stenson, P. D.; Yavuz, A.; Buluş, H.; Günel, M.; Friedman, J. M.; Özçelik, Tayfun
The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 30% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.
Open Access
A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection
(Elsevier, 2020) Casanova, J.-L.; Su, H. C.; Abel, L.; Aiuti, A.; Almuhsen, S.; Arias, A. A.; Bastard, P.; Biggs, C.; Bogunovic, D.; Boisson, B.; Boisson-Dupuis, S.; Bolze, A.; Bondarenko, A.; Bousfiha, A.; Brodin, P.; Bustamante, J.; Butte, M.; Casari, G.; Ciancanelli, M.; Cobat, A.; Condino-Neto, A.; Cooper, M.; Dalgard, C.; Espinosa, S.; Feldman, H.; Fellay, J.; Franco, J. L.; Hagin, D.; Itan, Y.; Jouanguy, E.; Lucas, C.; Mansouri, D.; Meyts, I.; Milner, J.; Mogensen, T.; Morio, T.; Ng, L.; Notarangelo, L. D.; Okada, S.; Özçelik, Tayfun; Palacín, P. S.; Planas, A.; Prando, C.; Puel, A.; Pujol, A.; Redin, C.; Renia, L.; Gallego, J. C. R.; Quintana-Murci, L.; Sancho-Shimizu, V.; Sankaran, V.; Seppänen, M. R. J.; Shahrooei, M.; Snow, A.; Spaan, A.; Tangye, S.; Tur, J. P.; Turvey, S.; Vinh, D. C.; von Bernuth, H.; Wang, X.; Zawadzki, P.; Zhang, Q.; Zhang, S.
SARS-CoV-2 infection displays immense inter-individual clinical variability, ranging from silent infection to lethal disease. The role of human genetics in determining clinical response to the virus remains unclear. Studies of outliers—individuals remaining uninfected despite viral exposure and healthy young patients with life-threatening disease—present a unique opportunity to reveal human genetic determinants of infection and disease.
Open Access
Human CRY1 variants associate with attention deficit/hyperactivity disorder
(American Society for Clinical Investigation, 2020) Onat, O. Emre; Kars, M. Ece; Gül, Ş.; Bilguvar, K.; Wu, Y.; Özhan, Ayşe; Aydın, C.; Başak, A. N.; Trusso, M. A.; Goracci, A.; Fallerini, C.; Renieri, A.; Casanova, J-L.; Itan, Y.; Atbaşoğlu, C. E.; Saka, M. C.; Kavaklı, İ. H.; Özçelik, Tayfun
Attention deficit/hyperactivity disorder (ADHD) is a common and heritable phenotype frequently accompanied by insomnia, anxiety, and depression. Here, using a reverse phenotyping approach, we report heterozygous coding variations in the core circadian clock gene cryptochrome 1 in 15 unrelated multigenerational families with combined ADHD and insomnia. The variants led to functional alterations in the circadian molecular rhythms, providing a mechanistic link to the behavioral symptoms. One variant, CRY1Δ11 c.1657+3A>C, is present in approximately 1% of Europeans, therefore standing out as a diagnostic and therapeutic marker. We showed by exome sequencing in an independent cohort of patients with combined ADHD and insomnia that 8 of 62 patients and 0 of 369 controls carried CRY1Δ11. Also, we identified a variant, CRY1Δ6 c.825+1G>A, that shows reduced affinity for BMAL1/CLOCK and causes an arrhythmic phenotype. Genotype-phenotype correlation analysis revealed that this variant segregated with ADHD and delayed sleep phase disorder (DSPD) in the affected family. Finally, we found in a phenome-wide association study involving 9438 unrelated adult Europeans that CRY1Δ11 was associated with major depressive disorder, insomnia, and anxiety. These results defined a distinctive group of circadian psychiatric phenotypes that we propose to designate as “circiatric” disorders.
Open Access
Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common TYK2 missense variant
(NLM (Medline), 2018) Boisson-Dupuis, S.; Ramirez-Alejo, N.; Li, Z.; Patin, E.; Rao, G.; Kerner, G.; Lim, C. K.; Krementsov, D. N.; Hernandez, N.; Ma, C. S.; Zhang, Q.; Markle, J.; Martinez-Barricarte, R.; Payne, K.; Fisch, R.; Deswarte, C.; Halpern, J.; Bouaziz, M.; Mulwa, J.; Sivanesan, D.; Lazarov, T.; Naves, R.; Garcia, P.; Itan, Y.; Boisson, B.; Checchi, A.; Jabot-Hanin, F.; Cobat, A.; Guennoun, A.; Jackson, C. C.; Pekcan, S.; Çalışkaner, Z.; Inostroza, J.; Costa-Carvalho, B. T.; De Albuquerque, J. A. T.; Garcia-Ortiz, H.; Orozco, L.; Özçelik, Tayfun; Abid, A.; Rhorfi, I. A.; Souhi, H.; Amrani, H. N.; Zegmout, A.; Geissmann, F.; Michnick, S. W.; Muller-Fleckenstein, I.; Fleckenstein, B.; Puel, A.; Ciancanelli, M. J.; Marr, N.; Abolhassani, H.; Balcells, M. E.; Condino-Neto, A.; Strickler, A.; Abarca, K.; Teuscher, C.; Ochs, H. D.; Reisli, I.; Sayar, E. H.; El-Baghdadi, J.; Bustamante, J.; Hammarström, L.; Tangye, S. G.; Pellegrini, S.; Quintana-Murci, L.; Abel, L.; Casanova, J. -L.
Inherited IL-12Rβ1 and TYK2 deficiencies impair both IL-12- and IL-23-dependent IFN-γ immunity and are rare monogenic causes of tuberculosis, each found in less than 1/600,000 individuals. We show that homozygosity for the common TYK2 P1104A allele, which is found in about 1/600 Europeans and between 1/1000 and 1/10,000 individuals in regions other than East Asia, is more frequent in a cohort of patients with tuberculosis from endemic areas than in ethnicity-adjusted controls (P = 8.37 × 10-8; odds ratio, 89.31; 95% CI, 14.7 to 1725). Moreover, the frequency of P1104A in Europeans has decreased, from about 9% to 4.2%, over the past 4000 years, consistent with purging of this variant by endemic tuberculosis. Surprisingly, we also show that TYK2 P1104A impairs cellular responses to IL-23, but not to IFN-α, IL-10, or even IL-12, which, like IL-23, induces IFN-γ via activation of TYK2 and JAK2. Moreover, TYK2 P1104A is properly docked on cytokine receptors and can be phosphorylated by the proximal JAK, but lacks catalytic activity. Last, we show that the catalytic activity of TYK2 is essential for IL-23, but not IL-12, responses in cells expressing wild-type JAK2. In contrast, the catalytic activity of JAK2 is redundant for both IL-12 and IL-23 responses, because the catalytically inactive P1057A JAK2, which is also docked and phosphorylated, rescues signaling in cells expressing wild-type TYK2. In conclusion, homozygosity for the catalytically inactive P1104A missense variant of TYK2 selectively disrupts the induction of IFN-γ by IL-23 and is a common monogenic etiology of tuberculosis. Copyright